GWAS-informed genomic selection for cold tolerance in pepper (Capsicum annuum L.)

Area of Science:

• Plant breeding and genetics
• Climate change adaptation
• Genomic selection strategies

Background:

• Pepper (Capsicum annuum L.) cold tolerance is crucial for climate change adaptation, but breeding is limited by phenotyping challenges and complex genetics.
• Genomic selection (GS) can accelerate genetic gain, but its predictive ability is often reduced by uninformative markers in whole-genome sets.

Purpose of the Study:

• To develop a robust phenotypic index for adult-stage cold tolerance in pepper.
• To implement a genome-wide association study (GWAS)-informed genomic selection (GS) strategy to improve prediction accuracy.

Main Methods:

• Phenotyped 192 pepper accessions for cold tolerance using a visual survival score (Surv) and a composite cold-tolerance index (CTI).
• Performed genome-wide association study (GWAS) to identify candidate genomic regions associated with cold tolerance.
• Applied nested cross-validation (CV) and leave-one-out CV (LOOCV) using GWAS-selected marker sets for genomic prediction.

Main Results:

• Both CTI and Surv exhibited moderate heritability (h² ≈ 0.55 and 0.53, respectively), indicating significant additive genetic variance.
• GWAS identified 13 candidate genomic regions, including genes like TRM9, CAP1, and PP2A-2, linked to abiotic stress responses.
• GWAS-selected marker sets achieved higher prediction accuracies (e.g., 0.349 for CTI in LOOCV) compared to full or random marker sets.

Conclusions:

• The CTI effectively assesses cold tolerance, revealing hidden genetic variation by converting ordinal survival data into a continuous spectrum.
• The integrated GWAS-informed GS framework successfully identified candidate genes and improved prediction efficiency for complex traits.
• This approach provides a practical strategy for understanding adult-stage cold tolerance genetics and enhancing genomic prediction in pepper breeding.